Automatic network reconstruction from experimental time-series data: A survey

Annegret Wagler

doi:10.1515/itit-2013-1020

Article

Automatic network reconstruction from experimental time-series data: A survey

Annegret Wagler
Annegret Wagler received the PhD Degree from the University of Technology Berlin in 2000. From 2000 to 2004, she was post-doc at the Zuse Institute Berlin. From 2004 to 2010, she was the head of a junior research group at the Otto-von-Guericke-University Magdeburg and habilitated in 2007. In September 2010, she got a professor position at the University Blaise Pascal (Clermont-Ferrand II) and a chair of excellence of CNRS.
CNRS and Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Université Blaise Pascal (Clermont-Ferrand II), Campus scientifique des Cézeaux Bat. ISIMA, 63173 Aubière, France, Tel.: +33 (0) 473 40 5367, Fax: +33 (0) 473 40 5001

Published/Copyright: March 31, 2014

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From the journal it – Information Technology Volume 56 Issue 2

Abstract

The reconstruction of models from experimental data is a challenging problem due to the inherited complexity of the studied biological systems. We discuss an exact, exclusively data-driven approach to reconstruct Petri nets, a framework which turned out to coherently model static interactions and dynamic processes. The reconstructed models shall reproduce the experimentally observed dynamic behavior in a simulation. For that, we consider Petri nets with two types of extensions, priority relations among the transitions and control-arcs, to obtain additional activation rules that control the dynamic behavior. Here, we give an overview on results concerning the reconstruction of standard networks with and without priorities, extended Petri nets, and extended Petri nets with priorities. All these approaches aim at reconstructing all networks of the studied type that fit the given experimental data, to provide all possible alternatives of mechanisms behind the experimentally observed phenomena.

Keywords: ACM CCS→Mathematics of computing→Discrete mathematics→Combinatorics; ACM CCS→Mathematics of computing→Numerical analysis

About the author

Annegret Wagler

Annegret Wagler received the PhD Degree from the University of Technology Berlin in 2000. From 2000 to 2004, she was post-doc at the Zuse Institute Berlin. From 2004 to 2010, she was the head of a junior research group at the Otto-von-Guericke-University Magdeburg and habilitated in 2007. In September 2010, she got a professor position at the University Blaise Pascal (Clermont-Ferrand II) and a chair of excellence of CNRS.

CNRS and Laboratoire d'Informatique, de Modélisation et d'Optimisation des Systèmes (LIMOS), Université Blaise Pascal (Clermont-Ferrand II), Campus scientifique des Cézeaux Bat. ISIMA, 63173 Aubière, France, Tel.: +33 (0) 473 40 5367, Fax: +33 (0) 473 40 5001

Received: 2013-7-9

Accepted: 2014-2-11

Published Online: 2014-3-31

Published in Print: 2014-4-28

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Articles in the same Issue

https://doi.org/10.1515/itit-2013-1020

Keywords for this article

ACM CCS→Mathematics of computing→Discrete mathematics→Combinatorics; ACM CCS→Mathematics of computing→Numerical analysis